Django Genome
Django app for syncing and storing human genome reference data
Documentation
The full documentation is at https://django-genome.readthedocs.io.
Quickstart
Install Django Genome:
pip install django-genome
Add it to your INSTALLED_APPS (along with DRF and django-filters):
INSTALLED_APPS = (
...
'rest_framework',
'django_filters',
...
'genome',
...
)Add Django Genome’s URL patterns:
from genome import urls as genome_urls
urlpatterns = [
...
url(r'^', include(genome_urls, namespace='genome')),
...
]Initial sync for genome models:
python manage.py genome_sync
Features
Includes models for Genome, Chromosome, CytoBand, Gene, Transcript, and Exons
Syncs data for hg18, hg19, hg38 from HGNC and UCSC
Running Tests
Does the code actually work?
source <YOURVIRTUALENV>/bin/activate (myenv) $ pip install tox (myenv) $ tox
Credits
Tools used in rendering this package:
History
0.1.0 (2017-12-30)
First release on PyPI.
Initial models and REST API
Syncs data from HGNC and UCSC to build database
0.2.0 (2018-01-05)
Improved REST API Filters
made Chromosomes and Gene Symbols save as uppercase to maintain consistency
0.2.1 (2018-01-08)
Fixed issues with migrations
0.2.2 (2018-01-12)
Fixed route names for SimpleRouter
0.3.0 (2018-02-09)
Updated requirements to the latest
0.4.0 (2018-03-30)
Added API for chromosomes
Changed gene_symbol from being unique
0.5.0 (2018-04-04)
Added GraphQL Nodes
0.6.0 (2018-04-07)
Added support for Django 2 and Python 3.6
Dropped support for Django < 1.11 and Python 2.7, 3.3, 3.4
0.6.1 (2018-04-18)
Updated 3rd party libs
0.6.2 (2018-05-14)
Updated chromosomes sync to ensure lexicographic ordering of chromosomes
0.6.3 (2018-05-16)
Updated sync to be able to skip sync of exons
0.6.4 (2018-05-16)
Updated setup.py to read requirements.txt
0.7.0 (2018-06-01)
Added Gene List model
Removed support for GraphQL - this is not needed here. Applications that import this package can set up Nodes/Schema using models
0.7.1 (2018-06-07)
#54 - Updated management methods to allow for updating when retrieving latest changes from RefSeq
#56 - Updated Gene model to have property ensembl_gene_id - which will check HGNC and Ensembl provided gene Ids
0.7.2 (2018-08-13)
Updated 3rd party requirements. Some requirements had changed so it was causing failures
0.7.3 (2018-09-26)
Updated transcript model to include preferred transcript boolean
0.7.4 (2018-10-29)
Updated 3rd party libs
0.7.6 (2018-11-27)
HGNC changed their headers - so gene sync was broken. Made reading headers case insensitive
0.7.7 (2019-02-08)
Updated 3rd party libs
Updated tests to use py.test fixtures correctly
0.7.8 (2019-04-10)
Updated 3rd party libs
Updated travis to use xenial distribution. Django 2.1 dropped support for SQLite < 3.8.3
0.8.0 (2019-05-31)
Refactored sync to use UCSC MySQL database connection
Updated sync to incorporate transcript refseq versions
Updated package to use latest cookiecutter template
0.8.1 (2019-06-14)
Gene entries created from RefSeq where not setting the chromosome attribute
Added better logging functionality
0.8.2 (2019-07-26)
Updated 3rd party libs
0.9.0 (2019-08-02)
Updated Gene data model and sync to include date approved/modified.
0.9.1 (2019-08-05)
Fixed issue with bundle not being published correctly
0.9.2 (2019-08-09)
Updated 3rd party libs
0.9.3 (2019-09-09)
Updated 3rd party libs
1.0.0 (2019-11-01)
Updated Gene model to make sure it is unique on symbol
First, production release
1.1.0 (2019-11-26)
Updated dependencies
1.1.1 (2020-03-12)
#149 - Updated the genome sync to deal with new headers
#144 - preferred transcript sync will now use version numbers
1 maintainer
Metadata
1 maintainer
Release files for django-genome 1.1.1
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